Why is part of a mesh a different color on the viewport?
Normally, I believe it's just plain shadows that blender generates for you to be able to identify the object as 3D. However in this case, the unusual colouring of these faces are most likely because their normals are the wrong way around. If your model is well designed (in which you made sure all the edges connect each other with no holes or gaps, which can be re-ensured using remove doubles in edit mode, but don't do this if you actually need different vertices in the same place), go to edit mode, click the UV tab on the left and recalculate normals.

Or to avoid any confusion, click Reverse normals on the faces that look unusually dark. If they become brighter and more grey rather than blue, it means their UV's were the wrong way around and are now the right way around. This is essential when importing models into game engines like Unity 3D, where you wouldn't want to have a partially invisible asset.

Here: